Transcriptome size matters for single-cell RNA-seq normalization and bulk deconvolution

• DOI: 10.1038/s41467-025-56623-1
• Publication Date: 2025-02-01T14:01:10Z
• Authors: Songjian Lu; Jiyuan Yang; Lei Yan; Jingjing Liu; Judy Jiaru Wang; Rhea Jain; Jiyang Yu
• Keywords: Science; Q; Article

Abstract The variation of transcriptome size across cell types significantly impacts single-cell RNA sequencing (scRNA-seq) data normalization and bulk RNA-seq cellular deconvolution, yet this intrinsic feature is often overlooked. Here we introduce ReDeconv, a computational algorithm that incorporates transcriptome size into scRNA-seq normalization and bulk deconvolution. ReDeconv introduces a scRNA-seq normalization approach, Count based on Linearized Transcriptome Size (CLTS), which corrects differential expressed genes typically misidentified by standard count per 10 K normalization, as confirmed by orthogonal validations. By maintaining transcriptome size variation, CLTS-normalized scRNA-seq enhances the accuracy of bulk deconvolution. Additionally, ReDeconv mitigates gene length effects and models expression variances, thereby improving deconvolution outcomes, particularly for rare cell types. Evaluated with both synthetic and real datasets, ReDeconv surpasses existing methods in precision. ReDeconv alters the practice and provides a new standard for scRNA-seq analyses and bulk deconvolution. The software packages and a user-friendly web portal are available.